Except 'God directed' evolution has the same evidence as Theory of Evolution, as essentially they are the same with respect to everything else- although 'God directed' is an extra assumption (although a replacement for 'random' which is also an assumption).
To some extent that is true, but scientific theories have no supernatural elements. To say "I believe in science, save that I replace their naturalistic explanation with this supernatural element" is very much to say that the scientific theory is wrong. The two then have very different implications. If god directed our evolution, for example, then this is it. If random mutation did it, then it is very much certain that we will continue to evolve, and this "humanity" of ours is in no sense a final form. Indeed, it is entirely possible that we will evolve into an unintelligent species of primate, if the environment favored the loss of intelligence...whereas it is very difficult to imagine why God would evolve intelligence into us and then take it away.
The curious thing is why God mimics random chance so that His changes are so often so poorly designed. Human knees for example? Prone to injury, same with our backs--they are not well designed for bipedal locomotion. Few engineers working from scratch would design a bipedal robot using the system that God chose, yet the design makes more sense if you imagine we evolved randomly, as then the design flaws are just a reflection the fact that the process has no true design.
Rather than build a durable life form, nature has fragile life forms hat procreate in great numbers, which sours futher evolution is random chance is at work (since more copies of DNA mean more room for mutations), but it is very hard on the individual, who has to live a fragile existence and suffer the deleterious effects that most mutations have (when they have any effect at all). As a strategy for God, though, who does not need mutation to occur randomly, there is really no need to pursue the numbers game.
Similarly, why do so many mutations have no effect? If they are random, it makes sense, not all our DNA codes for proteins. If they are directed, why does God mutate DNA purposefully, but to no effect.
It seems like God is hiding his hand by making himself look random. That's fine, but thee is clear evidence that suggests randomness as a result, and so it is strange that taking that inference and positing random mutations occur is somehow just as much an assumption as "God did it."
Religion is not the nullification of the natural.. They can perfectly compliment each other.
That is true, but that does not negate the fact that "God directed human evolution" is a supernaturalistic theory, and for that reason it's not science. Moreover, if one believes in God directed evolution, then one must believe that the science is
wrong. It may "appear" to be right because God is mimicking random mutation, but in fact the science is in fact an incorrect theory of the world.
There's nothing philosophically wrong with that position. It is entirely valid, even though it not something that one should teach in a science class. (Then again, assuming it were true, the alternative is to teach something in science class that is false.) My point is that I think more people are Intelligent Design proponents than realize it. I think most people think they believe in the science, but really don't and think God guides the process.